How critical is ncs operator for real space refinement

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Re: [phenixbb] How critical is ncs...

Yangqi Gu

21 Jan 2020 21 Jan '20

4:32 a.m.

Dear PHENIX developers, I have a question about NCS operator. Since I have a cryo-EM map and I want to refine my filament coordinates within the map. I generated the coordinate map manually in Chimera by building multiple chains with rigid body refinement. Since I did not generate the NCS operator file (I tried by doing map symmetry, it did not give me the right helical symmetry), I did not refine with ncs restraints. I am wondering in this case, how critical it is to refine a model with helical symmetry applied. Is it a must or can I go with the way I did? Hope to hear from you soon! Best, Yangqi

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Tom Terwilliger

21 Jan 21 Jan

2:20 p.m.

New subject: How critical is ncs operator for real space refinement

Hi Yangqi, You don't actually need the NCS relationships in order to refine with NCS restraints because the default is to use torsion-angle restraints which only use local relationships, not overall NCS matrices. So you can go ahead and use your rigid-body-refined starting model with torsion-angle restraints in phenix.real_space_refine. That will not impose perfect helical restraints, but I am guessing that your map already has near-perfect helical symmetry so that should not matter very much. Also you might first run with just one monomer which will be much quicker and give you almost the same answer. Let us know if that does not do it! All the best, Tom T On Mon, Jan 20, 2020 at 9:33 PM Yangqi Gu wrote:

...

Dear PHENIX developers, I have a question about NCS operator. Since I have a cryo-EM map and I want to refine my filament coordinates within the map. I generated the coordinate map manually in Chimera by building multiple chains with rigid body refinement. Since I did not generate the NCS operator file (I tried by doing map symmetry, it did not give me the right helical symmetry), I did not refine with ncs restraints. I am wondering in this case, how critical it is to refine a model with helical symmetry applied. Is it a must or can I go with the way I did? Hope to hear from you soon! Best, Yangqi

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-- Thomas C Terwilliger Laboratory Fellow, Los Alamos National Laboratory Senior Scientist, New Mexico Consortium 100 Entrada Dr, Los Alamos, NM 87544 Email: [email protected] Tel: 505-431-0010

Tom Terwilliger

7:38 p.m.

New subject: How critical is ncs operator for real space refinement

Hi Yangqi, I gave you an incorrect answer about phenix.real_space_refinement. Here is Pavel's clarification: NCS is used as constraints in real-space refinement, NCS restraints (torsion, Cartesian) are not available in real-space refinement. NCS copies are found automatically unless the user provides their own selections. NCS operators are figures out internally and optionally can be refined. If NCS constraints are used all NCS copies will be identical after refinement (RMSD after superposition is exactly 0). All the best, Tom T On Mon, Jan 20, 2020 at 9:33 PM Yangqi Gu wrote:

...

Dear PHENIX developers, I have a question about NCS operator. Since I have a cryo-EM map and I want to refine my filament coordinates within the map. I generated the coordinate map manually in Chimera by building multiple chains with rigid body refinement. Since I did not generate the NCS operator file (I tried by doing map symmetry, it did not give me the right helical symmetry), I did not refine with ncs restraints. I am wondering in this case, how critical it is to refine a model with helical symmetry applied. Is it a must or can I go with the way I did? Hope to hear from you soon! Best, Yangqi

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

-- Thomas C Terwilliger Laboratory Fellow, Los Alamos National Laboratory Senior Scientist, New Mexico Consortium 100 Entrada Dr, Los Alamos, NM 87544 Email: [email protected] Tel: 505-431-0010

Yangqi Gu

7:53 p.m.

New subject: How critical is ncs operator for real space refinement

Hi Tom and Pavel, Thank you for your help. I think I have a much better understanding what I should do now. I will try with your suggestions and I will let you know. Best, Yangqi On Tue, Jan 21, 2020 at 2:39 PM Tom Terwilliger < [email protected]> wrote:

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Hi Yangqi,

I gave you an incorrect answer about phenix.real_space_refinement. Here is Pavel's clarification:

NCS is used as constraints in real-space refinement, NCS restraints (torsion, Cartesian) are not available in real-space refinement.

NCS copies are found automatically unless the user provides their own selections. NCS operators are figures out internally and optionally can be refined.

If NCS constraints are used all NCS copies will be identical after refinement (RMSD after superposition is exactly 0).

All the best, Tom T

On Mon, Jan 20, 2020 at 9:33 PM Yangqi Gu wrote:

...
Dear PHENIX developers, I have a question about NCS operator. Since I have a cryo-EM map and I want to refine my filament coordinates within the map. I generated the coordinate map manually in Chimera by building multiple chains with rigid body refinement. Since I did not generate the NCS operator file (I tried by doing map symmetry, it did not give me the right helical symmetry), I did not refine with ncs restraints. I am wondering in this case, how critical it is to refine a model with helical symmetry applied. Is it a must or can I go with the way I did? Hope to hear from you soon! Best, Yangqi

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

-- Thomas C Terwilliger Laboratory Fellow, Los Alamos National Laboratory Senior Scientist, New Mexico Consortium 100 Entrada Dr, Los Alamos, NM 87544 Email: [email protected] Tel: 505-431-0010

-- Yangqi Gu Graduate Student Malvankar Lab Yale University, West Campus

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